Detection and Characterization of Anomalies in the 16S rRNA Gene Sequence of Phytoplasma Strains

Characterization of phytoplasmas is primarily based on sequence analysis of their highly conserved 16S rRNA gene sequences. Even minor changes in the sequence of 16S rRNA gene can elucidate long-term evolutionary events along with modification of ecological characteristics within bacterial communities. The presence of any error and anomalies in 16S rRNA gene sequences can confound downstream analyses such as taxonomy and phylogenetic analyses. The most common sequence anomalies in the bacterial 16S rRNA gene sequences are chimera and sequencing errors. This investigation employed bioinformatics tools to examine the presence of such anomalies in the 16S rRNA gene sequence of representative phytoplasma strains from more than 170 subgroups within 40 16Sr groups. The findings suggested that the 16S rRNA gene sequences of eight phytoplasma strains contained anomalies, characteristics of chimeras, or some sorts of sequencing errors. Most of these strains were resolved on atypically elongated branches in the phylogenetic tree. The most notable strains with likely anomalous 16S rRNA gene sequences were reference strains of ‘Ca. P. wodyetiae, ‘Ca. P. allocasuarinae’ and ‘Ca. P. lycopersici’ as well as representative strains of the 16Sr groups XXVI and XXVII. The findings of this study suggest that anomalous 16S rRNA gene sequences are probably not restricted to the eight strains detected by the bioinformatics tools employed in this study.